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On a dock in the middle of nowhere, an old man waits for a friend. Unfortunately, it's a Red Flagassassin who shows up instead.

One by one, the Alpha Team is taken down with tranquilizer darts and relocated to Binghamton, the facility for the "bad" Alphas they usually send away. When a shaky Dr. Rosen demands to know what's going on, he is granted an audience with Nathan Clay, who makes the claim that someone on Rosen's team is a Red Flag mole.

The old man murdered earlier was one of three scientists murdered the previous day, all involved with the MK-Ultra experiments, apparently tied to the government's involvement with Alphas. The files revealing the scientists' identities were in Rosen's possession, and a tracked signal showed them being transmitted from the team's office.

Clay talks to each of the team members, trying to ferret out the mole, but it doesn't work — even though he's also using Eric Latreaux, an Alpha-powered, human lie detector. Out of options, Clay throws the lot of them into a cafeteria, so the team can find the mole amongst themselves.

Clay's plan backfires, however, when the team uses a combination of their powers and some exaggerated pain on the part of Dr. Rosen to escape. Unwilling to kill the whole team, Clay must let them go and wait for round two. When the team regroups in an abandoned warehouse, tempers flare as they all accuse each other of being the mole. Suspicion comes to rest most heavily on Cameron Hicks, as Dr. Rosen explains about the numerous cash deposits Hicks has been making — a fact which Gary Bell discovered. With Clay and the rest of the DoD closing in fast, a fight erupts between Hicks and Bill Harken and Dr. Rosen gets punched in the face.

As Clay and his troops swoop in, Rachel Pirzad gets a good look at Rosen's spilled blood and realizes that he is not Dr. Rosen at all, but in fact their mole. The faux Dr. Rosen has already escaped back to the office with Gary, the only Alpha who can erase the MK Ultra files from the server.

Meanwhile, across town, the real Dr. Rosen wakes up and manages to get the drop on the Red Flag assassin who was about to put him down. Dr. Rosen goes straight to the office where he encounters his doppelganger and must convince a confused Gary who the real Dr. Rosen is. When Clay and the rest of the team show up, the Morphogene Alpha morphs into Gary and tries to slip past them, but Rachel sees through the ruse.

The tragedy has been averted, but Clay and the real Dr. Rosen are testy with each other over how the situation was handled. There is good news, though. Clay is going to let Eric freelance for the Alpha team. In reference to the mysterious cash deposits, Hicks finally admits to selling his baseball "fame" (two no-hitter games during his minor league days) for his son's college fund. Things are almost back to normal when Bill suddenly collapses in a heap.

Nathan Clay: Look, we had to bring you in with everybody else. Otherwise they would have been suspicious. Bill: You shot me--what--eighteen times? You did a really good job selling that.

Eric Letrobe: Hi, Rachel. It's Eric. Long time. Rachel: Eric Letrobe? I know him. We brought him here two years ago. Eric, what are you doing? Eric Letrobe: I'm reading your micro-expressions. So far, so good. Clay said if I help out, he'll get me out of this dump. So maybe once I get out, you and I can catch a movie. Rachel: Eric, would you please tell Clay that I'm telling the truth? Eric Letrobe: Or maybe a show. Le Miz, or The Producers. 'Cause I know a guy. Rachel: Eric, I don't even think those shows are running anymore. Nathan Clay: If the two of you are done, I'm trying to conduct an investigation.

Hicks: Hey, Eric! How's life treating you in here, huh? Nice and comfy? Eric Letrobe: The food's crap. Nathan Clay: I've had it before. It's not that bad. Eric Letrobe: Look me in the eye and say that.

Nina: Gary doesn't lie. Bill: We all know Gary doesn't lie. Gary: No, I do lie. I've been practicing. It's a social skill. Like the other day when I said I was going to have a pudding pop. I was lying. 'Cause I don't like pudding pops. That was a lie. I do like pudding pops. Rachel: Gary... Gary: I just knew we didn't have any.

Eric Letrobe: Hey, is there a bathroom around here? Hey, it's my downside. When I get nervous, I have to pee. Nathan Clay: No, your downside is that you're a distrustful, depressed miserable human being. Eric Letrobe: Oh, yeah. That.

Gary: Oh, that's gross. Dr. Rosen, don't do that in there? Are you sick? Creighton/"Rosen": No, I'm fine. Gary: No, you're not fine. Vomit is the body's way of telling us that we're not fine. Creighton/"Rosen": Do you ever shut up?!? Gary: But that won't grow anymore now, Dr. Rosen. It's delicate. It's a philodendron.

Rachel: Where is Gary? Gary: I'm here. I'm the real me. He's the fake. He was the fake Rosen before, but the real Dr. Rosen is here now. And he's hurt his leg and he has bad hair. Oh, yeah.